On the left is a floating table of contents for navigating between major sections of output:
Within each major section, content is split into tabs that are spread horizontally across the screen. By default, the About tab for each section is showing. Click on any tab to see specifics.
This section contains tables and graphs, in separate tabs.
To detect errors in data sets, the information in this section should be reviewed by Reserve data practitioners. These results are meant to help you find issues that need to be corrected in the raw data, and decide whether plots or data should be removed from analyses (e.g., “off season” surveys, plots no longer monitored, restoration sites).
There were 0 rows with no data. These rows were removed from the dataset before further processing. If rows were removed, relevant information is in a table below.
If monitoring plots did not have data in at least 3 separate years, they were removed from the dataset before statistical analyses. These plots do appear in the plots and information in the Exploration/QAQC and Summary Bar Chart sections of this document, but were removed before Univariate and Multivariate analyses.
In this dataset, there were 0 such plots removed. If plots were removed, relevant information is in a table below.
There were 0 data points that were removed due to QA/QC flags. If data points were removed, relevant information is in a table below.
| Site | 2015 | 2016 | 2017 | 2018 | 2019 | 2020 |
|---|---|---|---|---|---|---|
| clmaj | 0 | 30 | 30 | 30 | 30 | 30 |
| juro high | 21 | 21 | 21 | 23 | 21 | 21 |
| juro low | 35 | 35 | 35 | 35 | 35 | 35 |
| juro mid | 40 | 40 | 40 | 40 | 40 | 40 |
| spalt | 27 | 27 | 27 | 27 | 27 | 27 |
| Vegetation_Zone | 2015 | 2016 | 2017 | 2018 | 2019 | 2020 |
|---|---|---|---|---|---|---|
| L-Low Marsh | 22 | 22 | 22 | 22 | 22 | 22 |
| T-Transition | 87 | 87 | 87 | 89 | 87 | 87 |
| P-Pools/Pannes | 5 | 5 | 5 | 5 | 5 | 5 |
| H-High Marsh | 6 | 6 | 6 | 6 | 6 | 6 |
| UE-Upland Edge | 3 | 3 | 3 | 3 | 3 | 3 |
| FT-Freshwater Tidal | 0 | 30 | 30 | 30 | 30 | 30 |
Make sure the colors below correctly represent which Vegetation Zones your plots belong to. If something looks wrong, it needs to be corrected in the ‘Station_Table’ tab of your data workbook.
EMI, Ecotone Migration Index, is the proportional cover of species/covers or species/cover groupings that are expected to increase within a vegetation zone as sea level rises. These species were identified by reserve staff, for each zone, in the ‘veg-specs.xlsx’ file.
Species considered to be ‘migrators’ within each zone are denoted by ‘x’ in the following table:
| Species | L-Low Marsh | T-Transition | P-Pools/Pannes | H-High Marsh | UE-Upland Edge |
|---|---|---|---|---|---|
| Unvegetated | X | X | X | X | |
| Spartina alterniflora | X | X | X | ||
| Juncus roemerianus | X | X | X | ||
| Agalinus maritima | X | ||||
| Baccharis halimifolia | X | ||||
| Batis maritima | X | ||||
| Borrichia frutescens | X | ||||
| Distichlis spicata | X | ||||
| Ipomoea sagittata | X | ||||
| Ipomoea sp. | X | ||||
| Iva frutescens | X | ||||
| Juncus sp. | X | ||||
| Limonium carolinianum | X | ||||
| Sabatia stellaris | X | ||||
| Salicornia depressa | X | ||||
| Spartina patens | X | ||||
| Spartina spartinae | X | ||||
| Sphagnum sp. | X |
This section contains summary graphics. The color palettes are
generated via the khroma R package and were developed to be
colorblind-friendly.
These summary figures tell a graphical story about current conditions and trends through time. There are two types of figure:
The species/groups identified by the Reserve for these graphs are (in order):
And so the groups appearing in the plots should be (alphabetically):
These were automatically calculated as the species having the highest mean cover, across all plots and dates.
One spatial graph was generated for each Site. This can be changed between the options of Site and Transect in the “More_Options” sheet of the “veg-specs.xlsx” file.
Each panel on the graphs represents an individual vegetation plot, showing 4 evenly spaced-through-time samples, of the species choices from the “Analysis_Specs” sheet of the “veg-specs.xlsx” file.
Plots without associated spatial locations will not be included in these graphics.
A tab will be generated for results of each response variable. The response variables consist of each of the (up to) 4 response variables identified in the Analysis Specs spreadsheet, (up to) 2 custom metrics identified in the Analysis Specs spreadsheet, EMI (Ecotone Migration Index), Species Richness, and Shannon-Weiner Diversity Index. You will see the same tables and graphics for each.
The main statistical model used is a linear mixed model, via
lme4::lmer(), with the form
y ~ Vegetation Zone + Time + Zone*Time + 1|Plot, where
y is the response variable given in the tab, and each
individual plot has a random intercept.
If only one vegetation zone is present in the data file, Vegetation
Zone is removed and the statistical model is simplified to
y ~ Time + 1|Plot.
The reserve-identified univariate response variables are:
Any custom metrics specified in the ‘Analysis_Specs’ sheet of the ‘veg-specs.xlsx’ file are calculated here, for inclusion in univariate analyses.
If you do not see a tab for a metric you believe you defined, look just below these bullet points to see if there are error messages showing up in little boxes that are different from other text - these may be helpful in troubleshooting. There are a few likely reasons for problems:
EMI, Ecotone Migration Index, is the proportional cover of species/covers or species/cover groupings that are expected to increase within a vegetation zone as sea level rises. These species were identified by reserve staff, for each zone, in the ‘veg-specs.xlsx’ file.
See the ‘EMI’ tab in the ‘Exploratory and QA/QC’ section of this document for a table of species considered to be ‘ecotone migrators’ for each zone.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 0.4475 | 0.4475 | 1 | 731.16 | 18.13 | 0 |
| Vegetation_Zone | 4.7897 | 0.9579 | 5 | 475.24 | 38.80 | 0 |
| Years_sinceStart:Vegetation_Zone | 1.9051 | 0.3810 | 5 | 731.16 | 15.43 | 0 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 0.0485 | 0.0081 | 0.033 | 0.064 | 6.0 | 731.1 | 0.0000 |
| T-Transition | 0.0725 | 0.0041 | 0.064 | 0.081 | 17.7 | 731.2 | 0.0000 |
| P-Pools/Pannes | -0.0053 | 0.0173 | -0.039 | 0.029 | -0.3 | 731.2 | 0.7596 |
| H-High Marsh | 0.0541 | 0.0157 | 0.023 | 0.085 | 3.4 | 731.2 | 0.0006 |
| UE-Upland Edge | -0.0216 | 0.0223 | -0.065 | 0.022 | -1.0 | 731.1 | 0.3341 |
| FT-Freshwater Tidal | 0.0000 | 0.0094 | -0.018 | 0.018 | 0.0 | 731.1 | 1.0000 |
| R2m | R2c |
|---|---|
| 0.664 | 0.738 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
Species Richness, calculated on all non-abiotic, non-dead, and
non-overstory columns; using the vegan package.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 160.0977 | 160.0977 | 1 | 731.06 | 123.45 | 0.0000 |
| Vegetation_Zone | 18.8745 | 3.7749 | 5 | 325.96 | 2.91 | 0.0138 |
| Years_sinceStart:Vegetation_Zone | 176.1839 | 35.2368 | 5 | 731.06 | 27.17 | 0.0000 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 0.0368 | 0.0586 | -0.078 | 0.152 | 0.6 | 731.0 | 0.5304 |
| T-Transition | 0.1199 | 0.0298 | 0.061 | 0.178 | 4.0 | 731.1 | 0.0001 |
| P-Pools/Pannes | 0.3238 | 0.1250 | 0.078 | 0.569 | 2.6 | 731.1 | 0.0098 |
| H-High Marsh | 0.6881 | 0.1139 | 0.465 | 0.912 | 6.0 | 731.1 | 0.0000 |
| UE-Upland Edge | 0.7870 | 0.1618 | 0.469 | 1.105 | 4.9 | 731.0 | 0.0000 |
| FT-Freshwater Tidal | 0.8493 | 0.0680 | 0.716 | 0.983 | 12.5 | 731.0 | 0.0000 |
| R2m | R2c |
|---|---|
| 0.446 | 0.666 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
Shannon-Weiner Diversity index, calculated on all non-abiotic,
non-dead, and non-overstory columns; using the vegan
package.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 12.2815 | 12.2815 | 1 | 731.03 | 146.03 | 0.0000 |
| Vegetation_Zone | 0.9379 | 0.1876 | 5 | 269.64 | 2.23 | 0.0516 |
| Years_sinceStart:Vegetation_Zone | 11.6558 | 2.3312 | 5 | 731.03 | 27.72 | 0.0000 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 0.0297 | 0.0149 | 0.000 | 0.059 | 2.0 | 731.0 | 0.0469 |
| T-Transition | 0.0419 | 0.0076 | 0.027 | 0.057 | 5.5 | 731.0 | 0.0000 |
| P-Pools/Pannes | 0.0624 | 0.0318 | 0.000 | 0.125 | 2.0 | 731.1 | 0.0505 |
| H-High Marsh | 0.1918 | 0.0290 | 0.135 | 0.249 | 6.6 | 731.0 | 0.0000 |
| UE-Upland Edge | 0.2196 | 0.0412 | 0.139 | 0.300 | 5.3 | 731.0 | 0.0000 |
| FT-Freshwater Tidal | 0.2315 | 0.0173 | 0.198 | 0.266 | 13.4 | 731.0 | 0.0000 |
| R2m | R2c |
|---|---|
| 0.412 | 0.709 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 150.2792 | 150.2792 | 1 | 731.03 | 3.71 | 0.0545 |
| Vegetation_Zone | 12186.0749 | 2437.2150 | 5 | 260.03 | 60.15 | 0.0000 |
| Years_sinceStart:Vegetation_Zone | 1918.1691 | 383.6338 | 5 | 731.03 | 9.47 | 0.0000 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | -2.5657 | 0.3274 | -3.208 | -1.923 | -7.8 | 731 | 0.0000 |
| T-Transition | -0.1517 | 0.1665 | -0.479 | 0.175 | -0.9 | 731 | 0.3624 |
| P-Pools/Pannes | 0.0000 | 0.6988 | -1.372 | 1.372 | 0.0 | 731 | 1.0000 |
| H-High Marsh | 0.0000 | 0.6364 | -1.249 | 1.249 | 0.0 | 731 | 1.0000 |
| UE-Upland Edge | 0.0000 | 0.9044 | -1.776 | 1.776 | 0.0 | 731 | 1.0000 |
| FT-Freshwater Tidal | 0.0000 | 0.3802 | -0.746 | 0.746 | 0.0 | 731 | 1.0000 |
| R2m | R2c |
|---|---|
| 0.52 | 0.774 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 1954.054 | 1954.054 | 1 | 731.08 | 8.20 | 0.0043 |
| Vegetation_Zone | 82119.867 | 16423.973 | 5 | 373.70 | 68.92 | 0.0000 |
| Years_sinceStart:Vegetation_Zone | 24887.239 | 4977.448 | 5 | 731.08 | 20.89 | 0.0000 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | -2.3022 | 0.7940 | -3.861 | -0.743 | -2.9 | 731.1 | 0.0039 |
| T-Transition | -7.4206 | 0.4038 | -8.213 | -6.628 | -18.4 | 731.1 | 0.0000 |
| P-Pools/Pannes | -0.5468 | 1.6947 | -3.874 | 2.780 | -0.3 | 731.1 | 0.7471 |
| H-High Marsh | 0.0955 | 1.5433 | -2.934 | 3.125 | 0.1 | 731.1 | 0.9507 |
| UE-Upland Edge | 0.0000 | 2.1935 | -4.306 | 4.306 | 0.0 | 731.1 | 1.0000 |
| FT-Freshwater Tidal | 0.3752 | 0.9221 | -1.435 | 2.186 | 0.4 | 731.1 | 0.6842 |
| R2m | R2c |
|---|---|
| 0.509 | 0.67 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 12.4416 | 12.4416 | 1 | 731.03 | 60.41 | 0.0000 |
| Vegetation_Zone | 0.9854 | 0.1971 | 5 | 266.86 | 0.96 | 0.4448 |
| Years_sinceStart:Vegetation_Zone | 53.6092 | 10.7218 | 5 | 731.03 | 52.06 | 0.0000 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 0.0000 | 0.0233 | -0.046 | 0.046 | 0.0 | 731 | 1.0000 |
| T-Transition | -0.0211 | 0.0119 | -0.044 | 0.002 | -1.8 | 731 | 0.0755 |
| P-Pools/Pannes | 0.8030 | 0.0498 | 0.705 | 0.901 | 16.1 | 731 | 0.0000 |
| H-High Marsh | 0.0000 | 0.0454 | -0.089 | 0.089 | 0.0 | 731 | 1.0000 |
| UE-Upland Edge | 0.0000 | 0.0645 | -0.127 | 0.127 | 0.0 | 731 | 1.0000 |
| FT-Freshwater Tidal | 0.0000 | 0.0271 | -0.053 | 0.053 | 0.0 | 731 | 1.0000 |
| R2m | R2c |
|---|---|
| 0.257 | 0.638 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 2945.338 | 2945.338 | 1 | 731.07 | 52.04 | 0 |
| Vegetation_Zone | 21108.025 | 4221.605 | 5 | 355.60 | 74.59 | 0 |
| Years_sinceStart:Vegetation_Zone | 6325.105 | 1265.021 | 5 | 731.07 | 22.35 | 0 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 0.0000 | 0.3870 | -0.760 | 0.760 | 0.0 | 731.1 | 1.0000 |
| T-Transition | -0.0203 | 0.1968 | -0.407 | 0.366 | -0.1 | 731.1 | 0.9180 |
| P-Pools/Pannes | 0.0000 | 0.8259 | -1.621 | 1.621 | 0.0 | 731.1 | 1.0000 |
| H-High Marsh | -0.5433 | 0.7521 | -2.020 | 0.933 | -0.7 | 731.1 | 0.4703 |
| UE-Upland Edge | -7.3813 | 1.0690 | -9.480 | -5.283 | -6.9 | 731.1 | 0.0000 |
| FT-Freshwater Tidal | -4.0854 | 0.4494 | -4.968 | -3.203 | -9.1 | 731.1 | 0.0000 |
| R2m | R2c |
|---|---|
| 0.478 | 0.662 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
This custom metric was calculated using the following formula:
Juncus roemerianus / (Spartina alterniflora
+ 1)
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 1688.119 | 1688.119 | 1 | 731.08 | 6.97 | 0.0085 |
| Vegetation_Zone | 81401.697 | 16280.339 | 5 | 365.95 | 67.22 | 0.0000 |
| Years_sinceStart:Vegetation_Zone | 27734.970 | 5546.994 | 5 | 731.08 | 22.90 | 0.0000 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | -1.4817 | 0.8005 | -3.053 | 0.090 | -1.9 | 731.1 | 0.0646 |
| T-Transition | -7.5498 | 0.4071 | -8.349 | -6.751 | -18.5 | 731.1 | 0.0000 |
| P-Pools/Pannes | -0.5470 | 1.7085 | -3.901 | 2.807 | -0.3 | 731.1 | 0.7489 |
| H-High Marsh | 0.0955 | 1.5559 | -2.959 | 3.150 | 0.1 | 731.1 | 0.9510 |
| UE-Upland Edge | 0.0000 | 2.2113 | -4.341 | 4.341 | 0.0 | 731.1 | 1.0000 |
| FT-Freshwater Tidal | 0.3752 | 0.9296 | -1.450 | 2.200 | 0.4 | 731.1 | 0.6866 |
| R2m | R2c |
|---|---|
| 0.491 | 0.663 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
These tabs are the multivariate analyses.
In this section, we use multivariate techniques to ordination to visualize and analyze plant community change through plot-level cover data across marsh zones.
The following species/groups were identified by the reserve as important loading factors to display on NMDS outputs.
Sometimes these species do not appear on the plots; usually that is because all data points for that species were 0 or very close to it.
Up to 8 species/groups could be identified specifically in outputs of these multivariate analyses. Reserve choices are:
| Vegetation_Zone | Start | End |
|---|---|---|
| L-Low Marsh | 2015 (22) | 2020 (22) |
| T-Transition | 2015 (87) | 2020 (87) |
| P-Pools/Pannes | 2015 (5) | 2020 (5) |
| H-High Marsh | 2015 (6) | 2020 (6) |
| UE-Upland Edge | 2015 (3) | 2020 (3) |
| FT-Freshwater Tidal | 2016 (30) | 2020 (30) |
| Unvegetated |
| Agalinus maritima |
| Andropogon sp. |
| Andropogon virginicus var. glaucus |
| Anthriscus sp. |
| Asclepias lanceolata |
| Aster sp. |
| Baccharis halimifolia |
| Batis maritima |
| Bidens mitis |
| Bidens sp. |
| Borrichia frutescens |
| Centella erecta |
| Cladium jamaicense |
| Cyperus sp. |
| Daucus sp. |
| Dichanthelium sp. |
| Digitalis sp. |
| Diodia sp. |
| Distichlis spicata |
| Eleocharis tuberculosa |
| Eriocaulon compressum |
| Fimbristylis sp. |
| Fuirena breviseta |
| Heterotheca sp. |
| Ilex sp. |
| Ilex vomitoria |
| Ipomoea sagittata |
| Ipomoea sp. |
| Iva frutescens |
| Juncus roemerianus |
| Juncus sp. |
| Limonium carolinianum |
| Ludwigia sp. |
| Mikania scandens |
| Morella cerifera |
| Osmunda regalis |
| Panicum virgatum |
| Paspalum floridanum |
| Paspalum sp. |
| Phyla nodiflora |
| Pinus elliottii |
| Pluchea foetida |
| Pluchea sp. |
| Polygala ramosa |
| Proserpinaca sp. |
| Rhexia lutea |
| Rhexia sp. |
| Rhynchospora corniculata |
| Rhynchospora elliottii |
| Rhynchospora fascicularis |
| Rhynchospora rarifolia |
| Rhynchospora sp. |
| Sabatia stellaris |
| Sagittaria lancifolia |
| Sagittaria latifolia |
| Salicornia depressa |
| Sapium sebiferum |
| Schoenplectus sp. |
| Scleria sp. |
| Setaria sp. |
| Setaria parviflora |
| Seutera angustifolia |
| Solidago sp. |
| Spartina alterniflora |
| Spartina patens |
| Spartina spartinae |
| Sphagnum sp. |
| Toxicodendron radicans |
| Triadica sebifera |
| Unknown |
| Unknown 2 |
| Verbena sp. |
| Woodwardia virginica |
| Xyris laxifolia |
| Xyris sp. |
H0: Community change (if any) between start and end is consistent across vegetation zones.
The interaction p-value (Vegetation_Zone:Time_group) is
what to look at here:
Time_group to determine whether, across all zones, the
community was different at the end of monitoring than at the
beginning.Permutations have been restricted so that time points are only permuted within a vegetation plot, and both time points for a plot are permuted together across vegetation zones.
If only one vegetation zone is present in the data file, the overall PERMANOVA will be skipped; look in the zone-wise PERMANOVA section below for results.
| Df | SumOfSqs | R2 | F | Pr(>F) | |
|---|---|---|---|---|---|
| Time_group | 1 | 3.4191 | 0.0833 | 57.1142 | 0.001 |
| Vegetation_Zone | 5 | 17.7434 | 0.4324 | 59.2790 | 0.001 |
| Time_group:Vegetation_Zone | 5 | 2.2721 | 0.0554 | 7.5909 | 0.001 |
| Residual | 294 | 17.6000 | 0.4289 | ||
| Total | 305 | 41.0345 | 1.0000 |
H0: No community difference between ‘start’ and ‘end’ within a vegetation zone.
Permutations have been restricted so time points are only permuted within a vegetation plot.
| Vegetation Zone | R2 | p.value | p.value_Bonferonni |
|---|---|---|---|
| L-Low Marsh | 0.1208 | 0.013 | 0.078 |
| T-Transition | 0.2781 | 0.001 | 0.006 |
| P-Pools/Pannes | 0.0226 | 0.702 | 1.000 |
| H-High Marsh | 0.3401 | 0.024 | 0.144 |
| UE-Upland Edge | 0.3769 | 0.200 | 1.000 |
| FT-Freshwater Tidal | 0.2260 | 0.001 | 0.006 |
H0: No difference in dispersion between groups.
This is important to check because one of the assumptions of PERMANOVA is homogeneity of dispersion. Dispersion is the multivariate equivalent of variance. If this assumption is violated, caution should be used in interpreting PERMANOVA results.
The test used here is PERMDISP, implemented with the
betadisper function of the vegan package.
| Df | Sum Sq | Mean Sq | F | N.Perm | Pr(>F) | |
|---|---|---|---|---|---|---|
| Groups | 11 | 0.58 | 0.05 | 2.31 | 999 | 0.011 |
| Residuals | 294 | 6.67 | 0.02 |
If the PERMDISP indicated significant difference in dispersions, you should further investigate the following outputs:
| Group | Mean Distance |
|---|---|
| L-Low Marsh; Start | 0.274 |
| L-Low Marsh; End | 0.173 |
| T-Transition; Start | 0.227 |
| T-Transition; End | 0.140 |
| P-Pools/Pannes; Start | 0.171 |
| P-Pools/Pannes; End | 0.148 |
| H-High Marsh; Start | 0.172 |
| H-High Marsh; End | 0.186 |
| UE-Upland Edge; Start | 0.315 |
| UE-Upland Edge; End | 0.159 |
| FT-Freshwater Tidal; Start | 0.197 |
| FT-Freshwater Tidal; End | 0.217 |
| Vegetation Zone | Start.dispersion | End.dispersion | NumDf | DenDf | F.val | N.Perm | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 0.272 | 0.175 | 1 | 42 | 4.1 | 999 | 0.0570 |
| T-Transition | 0.227 | 0.141 | 1 | 172 | 14.5 | 999 | 0.0010 |
| P-Pools/Pannes | 0.172 | 0.153 | 1 | 8 | 0.0 | 999 | 0.8310 |
| H-High Marsh | 0.177 | 0.187 | 1 | 10 | 0.0 | 999 | 0.8750 |
| UE-Upland Edge | 0.320 | 0.161 | 1 | 4 | 0.7 | 719 | 0.6014 |
| FT-Freshwater Tidal | 0.198 | 0.218 | 1 | 58 | 0.3 | 999 | 0.6010 |
SIMPER was run if:
The p-values determining the above logic are unadjusted. Due to the exploratory nature of these analyses, we did not adjust p-values for multiple comparisons
SIMPER output explanation:
The top 6 species in output are below.
“average” is the average contribution of that species to the Bray-Curtis distance between the two groups (note, this is not expressed in % and the column does not total to 1); “sd” is the standard deviation of the species’ contribution. “cumulative” is the cumulative % contribution for this species and all those above it in the table. Typically people only report species up to the one that brings “cumulative” over 0.7. “p” is a p-value for that species based on permutation tests. “mean_start” is the mean cover of that species in the starting year(s), and “mean_end” is the mean cover of the species in the last year(s) of monitoring.
| average | sd | cumulative | p | mean_start | mean_end | |
|---|---|---|---|---|---|---|
| Spartina alterniflora | 0.1428 | 0.0920 | 0.3879 | 0.043 | 40.2 | 28.4 |
| Unvegetated | 0.1171 | 0.0803 | 0.7061 | 0.001 | 40.2 | 60.5 |
| Juncus roemerianus | 0.1076 | 0.1121 | 0.9985 | 0.230 | 19.5 | 11.0 |
| Distichlis spicata | 0.0006 | 0.0026 | 1.0000 | 0.001 | 0.0 | 0.1 |
| Agalinus maritima | 0.0000 | 0.0000 | 1.0000 | 0.0 | 0.0 | |
| Andropogon sp. | 0.0000 | 0.0000 | 1.0000 | 0.0 | 0.0 |
| average | sd | cumulative | p | mean_start | mean_end | |
|---|---|---|---|---|---|---|
| Juncus roemerianus | 0.1778 | 0.1068 | 0.4508 | 0.001 | 60.0 | 32.3 |
| Unvegetated | 0.1599 | 0.0918 | 0.8562 | 0.001 | 34.3 | 61.4 |
| Spartina alterniflora | 0.0183 | 0.0467 | 0.9027 | 0.243 | 2.2 | 1.7 |
| Distichlis spicata | 0.0098 | 0.0325 | 0.9275 | 0.005 | 1.2 | 0.8 |
| Borrichia frutescens | 0.0089 | 0.0146 | 0.9501 | 0.002 | 0.5 | 1.6 |
| Spartina spartinae | 0.0070 | 0.0187 | 0.9678 | 0.320 | 0.5 | 0.9 |
| None |
|---|
| SIMPER not run |
| average | sd | cumulative | p | mean_start | mean_end | |
|---|---|---|---|---|---|---|
| Spartina patens | 0.1458 | 0.0901 | 0.3895 | 0.013 | 50.0 | 21.7 |
| Unvegetated | 0.1003 | 0.0658 | 0.6573 | 0.063 | 38.2 | 55.4 |
| Panicum virgatum | 0.0292 | 0.0233 | 0.7352 | 0.561 | 5.0 | 5.4 |
| Cladium jamaicense | 0.0222 | 0.0187 | 0.7945 | 0.348 | 3.3 | 5.0 |
| Baccharis halimifolia | 0.0181 | 0.0251 | 0.8427 | 0.189 | 2.5 | 1.7 |
| Agalinus maritima | 0.0083 | 0.0094 | 0.8650 | 0.001 | 0.0 | 1.7 |
| average | sd | cumulative | p | mean_start | mean_end | |
|---|---|---|---|---|---|---|
| Cladium jamaicense | 0.2139 | 0.1341 | 0.3571 | 0.1014 | 51.7 | 16.7 |
| Unvegetated | 0.1742 | 0.0773 | 0.6480 | 0.0014 | 26.0 | 60.8 |
| Spartina patens | 0.0708 | 0.0882 | 0.7662 | 0.4014 | 13.3 | 2.5 |
| Ilex vomitoria | 0.0333 | 0.0500 | 0.8219 | 0.0014 | 0.0 | 6.7 |
| Spartina spartinae | 0.0264 | 0.0339 | 0.8660 | 0.4014 | 5.0 | 0.8 |
| Verbena sp. | 0.0167 | 0.0250 | 0.8938 | 0.0014 | 3.3 | 0.0 |
| average | sd | cumulative | p | mean_start | mean_end | |
|---|---|---|---|---|---|---|
| Cladium jamaicense | 0.1386 | 0.1062 | 0.3423 | 0.002 | 35.5 | 16.7 |
| Unvegetated | 0.1211 | 0.0808 | 0.6414 | 0.004 | 64.0 | 54.3 |
| Spartina patens | 0.0600 | 0.0526 | 0.7896 | 0.001 | 0.0 | 12.0 |
| Dichanthelium sp. | 0.0367 | 0.0311 | 0.8801 | 0.001 | 0.0 | 7.3 |
| Panicum virgatum | 0.0129 | 0.0299 | 0.9120 | 0.001 | 0.0 | 2.6 |
| Juncus roemerianus | 0.0083 | 0.0273 | 0.9326 | 0.001 | 0.0 | 1.7 |
In this section, NMDS is performed on data from only the starting and ending years for each vegetation zone. This tab essentially illustrates the PERMANOVA results. For NMDS with all years, see the tab ‘NMDS - all years’.
Non-metric multidimensional scaling is an ordination method that preserves ranked dissimilarities between observations. Exact calculated distances are not preserved in this type of ordination. Points that are closer together on the graphs are more similar than points that are further away, so NMDS is good for seeing groupings and gradients when present. For more information, see the sources referenced below.
This NMDS used Bray-Curtis dissimilarity on the full species matrix (see ‘About’ tab for list of species included), and 3 dimensions.
Final 3-dimensional NMDS stress was 0.0647.
Rules of thumb for interpreting stress, based on the sources below, are:
For more information on NMDS:
Clarke, K. R. (1993). Non-parametric multivariate analyses of changes in community structure. Australian Journal of Ecology, 18(1), Article 1. https://doi.org/10.1111/j.1442-9993.1993.tb00438.x
Clarke, K. R., & Warwick, R. M. (2001). Change in Marine Communities: An Approach to Statistical Analysis and Interpretation, 2nd ed. - Chapter 5 focuses on NMDS.
Zuur, A. F., Ieno, E. N., & Smith, G. M. (2007). Analysing ecological data. Springer. - Chapter 15 for NMDS.
(first two axes only)
The below plots, rather than using arrows for individual species or
vegetation groups, create contours for the specific values of each.
Contours are labeled with % cover values and are fit as a spline-based
surface using vegan::ordisurf().
This 3-d plot is interactive - you can zoom in and rotate the view. Each point represents a single vegetation plot at a single time point (start, open circles; or end, filled circles). Point color represents the plot’s vegetation zone. The red lines and labels represent the coordinates of species or species groups (centroid of comprising species) specified in the Analysis_Specs worksheet of the veg-specs.xlsx file.
No additional loadings specified. If you would like to graph additional environmental factors on the NMDS plot, please specify them in the ‘NMDS additional loadings’ section of the ‘More_Options’ sheet in the veg-specs.xlsx file.
By default, this analysis is not run because it may take more computing power than is available to perform ordination on many years worth of data points.
The all-years NMDS was attempted. If the results are not below, it simply didn’t work with your computer.
All measurements at all veg plots (with 3+ years of data) are represented. Centroids are calculated for each zone x year combination. Plots are zoomable. Two plots are provided: the first uses fixed axis scales, to emphasize where zone centroids are relative to each other in ordination space. The second uses free axis scales, to emphasize within-zone differences between years. There may not be much difference between these visually, depending on the spread of points within each zone. Zooming works differently in each. The loadings plot below applies to both graphs (the entire NMDS).
## R version 4.4.1 (2024-06-14 ucrt)
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